Man pages for fbreitwieser/pavian
Visualize and analyze metagenomics classification results

alignmentModuleServer part of alignment module
alignmentModuleUIUI part of alignment module
beautify_colnamesBeautify colnames
comparisonModuleServer part of comparison module
comparisonModuleUIUI part of the comparison module
dashboardUIFunction building dashboard UI, used in Shiny app
dataInputModuleServer part of pavian data input module.
dataInputModuleUIUI part of pavian data input module
filter_cladeReadsRemove specified taxa or whole clades this function removes...
filter_taxaFilter taxon
filter_taxonFilter lines from a kraken report result based on the...
get_nreadsGet number of aligned reads from a bam file
get_pileupGet the pileup-statistics from a bam file using Rsamtools
get_seqlengthsGet sequence lengths from a bam file
humanreadableMake a number human readable
load_or_createLoad a file from a cache directory, or create and save it
merge_reportsMerge report files into a wide format, with column(s) for...
merge_reports2Merge report files into a wide format, with column(s) for...
normalizeHelper function to normalize data
pavianServerPavian server function
plot_pileupPlot a pileup
read_reportRead Kraken-style and MetaPhlAn reports
read_report2Read kraken or centrifuge-style report
read_reportsRead metagenomics classification results ('reports'), with...
read_sample_dataRead sample definitions from a directory
read_server_directory1Search for classification results in a directory and its...
reportOverviewModuleShiny modules to display an overview of metagenomics reports
reportOverviewModuleUIUI part of report overview module
robust_zscoreCalculate robust z-score on matrix
runAppRun Pavian web interface
sampleModuleServer part for sample module
sampleModuleUIUI part for sample module
summarize_reportSummarize the result of a metagenomics report
summarize_reportsSummarize list of reports
zero_if_naHelper function that sets NAs to zeros in a supplied...
fbreitwieser/pavian documentation built on Dec. 27, 2018, 5:25 p.m.